% Rodent Brain-mask Segmentation tool
Detail description: The ‘RodentMRISkullStripping’ is a python module designed to provide an automatic rodent skull stripping. This module is a deep-learning-based framework, U-Net, to automatically identify the rodent brain boundaries in MR images. The whole framework is implemented using Keras with TensorFlow as the backend.
Plese install the following package before using RodentMRISkullStripping:
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numpy, tensorflow, and keras ex: conda install numpy tensorflow keras
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SimpleITK ex: conda install -c https://conda.anaconda.org/simpleitk SimpleITK
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scikit-image ex: conda install -c conda-forge scikit-image
Instruction:
- install RodentMRISKullStripping 'pip install rbm3==0.0.5'
- Give the input and output folder, you should put all the image in NIfTI format in the input folder . 'rbm3 -s 0.2 ' -s: image resolution, this option could resample the image resolution (i.e., 0.1, 0.2 isotropic resolution) in the UNet